Search Results - "Marchese, Doménica"

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions by Agostini, Federico, Zanzoni, Andreas, Klus, Petr, Marchese, Domenica, Cirillo, Davide, Tartaglia, Gian Gaetano

“…Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and…”
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Immune cell profiling of the cerebrospinal fluid enables the characterization of the brain metastasis microenvironment by Rubio-Perez, Carlota, Planas-Rigol, Ester, Trincado, Juan L., Bonfill-Teixidor, Ester, Arias, Alexandra, Marchese, Domenica, Moutinho, Catia, Serna, Garazi, Pedrosa, Leire, Iurlaro, Raffaella, Martínez-Ricarte, Francisco, Escudero, Laura, Cordero, Esteban, Cicuendez, Marta, Ruiz, Sara, Parra, Genís, Nuciforo, Paolo, Gonzalez, Josep, Pineda, Estela, Sahuquillo, Juan, Tabernero, Josep, Heyn, Holger, Seoane, Joan

“…Brain metastases are the most common tumor of the brain with a dismal prognosis. A fraction of patients with brain metastasis benefit from treatment with…”
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Advances in the characterization of RNA-binding proteins by Marchese, Domenica, de Groot, Natalia Sanchez, Lorenzo Gotor, Nieves, Livi, Carmen Maria, Tartaglia, Gian G.

“…From transcription, to transport, storage, and translation, RNA depends on association with different RNA‐binding proteins (RBPs). Methods based on…”
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Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease by Garrido-Trigo, Alba, Corraliza, Ana M., Veny, Marisol, Dotti, Isabella, Melón-Ardanaz, Elisa, Rill, Aina, Crowell, Helena L., Corbí, Ángel, Gudiño, Victoria, Esteller, Miriam, Álvarez-Teubel, Iris, Aguilar, Daniel, Masamunt, M. Carme, Killingbeck, Emily, Kim, Youngmi, Leon, Michael, Visvanathan, Sudha, Marchese, Domenica, Caratù, Ginevra, Martin-Cardona, Albert, Esteve, Maria, Ordás, Ingrid, Panés, Julian, Ricart, Elena, Mereu, Elisabetta, Heyn, Holger, Salas, Azucena

“…Ulcerative colitis and Crohn’s disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to…”
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Sampling time-dependent artifacts in single-cell genomics studies by Massoni-Badosa, Ramon, Iacono, Giovanni, Moutinho, Catia, Kulis, Marta, Palau, Núria, Marchese, Domenica, Rodríguez-Ubreva, Javier, Ballestar, Esteban, Rodriguez-Esteban, Gustavo, Marsal, Sara, Aymerich, Marta, Colomer, Dolors, Campo, Elias, Julià, Antonio, Martín-Subero, José Ignacio, Heyn, Holger

“…Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts…”
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Neurodegenerative diseases: quantitative predictions of protein-RNA interactions by Cirillo, Davide, Agostini, Federico, Klus, Petr, Marchese, Domenica, Rodriguez, Silvia, Bolognesi, Benedetta, Tartaglia, Gian Gaetano

“…Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework,…”
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FixNCut: single-cell genomics through reversible tissue fixation and dissociation by Jiménez-Gracia, Laura, Marchese, Domenica, Nieto, Juan C, Caratù, Ginevra, Melón-Ardanaz, Elisa, Gudiño, Victoria, Roth, Sara, Wise, Kellie, Ryan, Natalie K, Jensen, Kirk B, Hernando-Momblona, Xavier, Bernardes, Joana P, Tran, Florian, Sievers, Laura Katharina, Schreiber, Stefan, van den Berge, Maarten, Kole, Tessa, van der Velde, Petra L, Nawijn, Martijn C, Rosenstiel, Philip, Batlle, Eduard, Butler, Lisa M, Parish, Ian A, Plummer, Jasmine, Gut, Ivo, Salas, Azucena, Heyn, Holger, Martelotto, Luciano G

“…The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can…”
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Author Correction: Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease by Garrido-Trigo, Alba, Corraliza, Ana M., Veny, Marisol, Dotti, Isabella, Melón-Ardanaz, Elisa, Rill, Aina, Crowell, Helena L., Corbí, Ángel, Gudiño, Victoria, Esteller, Miriam, Álvarez-Teubel, Iris, Aguilar, Daniel, Masamunt, M. Carme, Killingbeck, Emily, Kim, Youngmi, Leon, Michael, Visvanathan, Sudha, Marchese, Domenica, Caratù, Ginevra, Martin-Cardona, Albert, Esteve, Maria, Ordás, Ingrid, Panés, Julian, Ricart, Elena, Mereu, Elisabetta, Heyn, Holger, Salas, Azucena

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Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein by Zanzoni, Andreas, Marchese, Domenica, Agostini, Federico, Bolognesi, Benedetta, Cirillo, Davide, Botta-Orfila, Maria, Livi, Carmen Maria, Rodriguez-Mulero, Silvia, Tartaglia, Gian Gaetano

“…Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory…”
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Discovering the 3' UTR-mediated regulation of alpha-synuclein by Marchese, Domenica, Botta-Orfila, Teresa, Cirillo, Davide, Rodriguez, Juan Antonio, Livi, Carmen Maria, Fernández-Santiago, Rubén, Ezquerra, Mario, Martí, Maria J, Bechara, Elias, Tartaglia, Gian Gaetano

“…Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions…”
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A Computational Approach for the Discovery of Protein-RNA Networks by Marchese, Domenica, Livi, Carmen Maria, Tartaglia, Gian Gaetano

“…Protein-RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes…”
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Albumin reprograms the B cell transcriptional landscape and improves neutrophil antimicrobial function in patients with decompensated cirrhosis by Clària, Joan, Aguilar, Ferran, Lozano, Juan-José, Jiménez-Gracia, Laura, Nieto, Juan C., Romero-Grimaldo, Berta, Marcos-Fa, Xavi, Giarracco, Emma, Weiss, Emmanuel, Trebicka, Jonel, Hernàndez, Inmaculada, Fernandez, Javier, Casulleras, Mireia, López-Vicario, Cristina, Muldur, Sinan, Hopke, Alex, Vlagea, Alexandru, Aransay, Ana M., Marchese, Domenica, Bernardi, Mauro, Jalan, Rajiv, Angeli, Paolo, Magri, Giuliana, Cerutti, Andrea, Irimia, Daniel, Heyn, Holger, Arroyo, Vicente, Moreau, Richard

“…Patients with acutely decompensated (AD) cirrhosis are immunocompromised and particularly susceptible to infections. This study investigated the…”
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3083 – SINGLE CELL MULTIOMIC ANALYSIS OF CLONAL AND TRANSCRIPTIONAL PROGRAMS OF CD19 CAR T CELLS IN THE IMMUNOTHERAPY RESPONSE by Murillo, Mercedes Guerrero, Rill-Hinarejos, Aina, Trincado, Juan L, Bataller, Alex, Ortiz-Maldonado, Valentin, Benitez-Ribas, Daniel, Español, Marta, González, Europa Azucena, Martinez-Cibrian, Nuria, Marchese, Doménica, Martín-Martín, Lourdes, Garcia-Sancho, Alejandro Martin, Heyn, Holger, Juan, Manel, Urbano-Ispizúa, Álvaro, Delgado, Julio, Orfao, Alberto, Mereu, Elisabetta, Bueno, Clara, Menendez, Pablo

“…CD19-directed CAR T-cell therapy has shown high rates of complete response against relapsed/refractory B-ALL, but it is only maintained in 50% of patients…”
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Integrative single-cell multi-omics of CD19-CARpos and CARneg T cells suggest drivers of immunotherapy response in B cell neoplasias by Guerrero-Murillo, Mercedes, Rill-Hinarejos, Aina, Trincado, Juan L., Bataller, Alex, Ortiz-Maldonado, Valentín, Benítez-Ribas, Daniel, Español-Rego, Marta, González-Navarro, E Azucena, Martínez-Cibrián, Nuria, Marchese, Doménica, Martín-Martín, Lourdes, Martín García-Sancho, Alejandro, Rives, Susana, Heyn, Holger, Juan, Manel, Urbano-Ispizúa, Álvaro, Delgado, Julio, Orfao, Alberto, Mereu, Elisabetta, Bueno, Clara, Menendez, Pablo

“…The impact of phenotypic, clonal, and functional heterogeneity of chimeric antigen receptor (CAR)-T cells on clinical outcome remains understudied. Here, we…”
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Integrative single-cell multi-omics of CD19-CAR pos and CAR neg T cells suggest drivers of immunotherapy response in B cell neoplasias by Guerrero-Murillo, Mercedes, Rill-Hinarejos, Aina, Trincado, Juan L, Bataller, Alex, Ortiz-Maldonado, Valentín, Benítez-Ribas, Daniel, Español-Rego, Marta, González-Navarro, E Azucena, Martínez-Cibrián, Nuria, Marchese, Doménica, Martín-Martín, Lourdes, Martín García-Sancho, Alejandro, Rives, Susana, Heyn, Holger, Juan, Manel, Urbano-Ispizúa, Álvaro, Delgado, Julio, Orfao, Alberto, Mereu, Elisabetta, Bueno, Clara, Menendez, Pablo

“…The impact of phenotypic, clonal, and functional heterogeneity of chimeric antigen receptor (CAR)-T cells on clinical outcome remains understudied. Here, we…”
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A single-cell tumor immune atlas for precision oncology by Nieto, Paula, Elosua-Bayes, Marc, Trincado, Juan L, Marchese, Domenica, Massoni-Badosa, Ramon, Salvany, Maria, Henriques, Ana, Nieto, Juan, Aguilar-Fernández, Sergio, Mereu, Elisabetta, Moutinho, Catia, Ruiz, Sara, Lorden, Patricia, Chin, Vanessa T, Kaczorowski, Dominik, Chan, Chia-Ling, Gallagher, Richard, Chou, Angela, Planas-Rigol, Ester, Rubio-Perez, Carlota, Gut, Ivo, Piulats, Josep M, Seoane, Joan, Powell, Joseph E, Batlle, Eduard, Heyn, Holger

“…The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune…”
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Detection of early seeding of Richter transformation in chronic lymphocytic leukemia by Nadeu, Ferran, Royo, Romina, Massoni-Badosa, Ramon, Playa-Albinyana, Heribert, Garcia-Torre, Beatriz, Duran-Ferrer, Martí, Dawson, Kevin J., Kulis, Marta, Diaz-Navarro, Ander, Villamor, Neus, Melero, Juan L., Chapaprieta, Vicente, Dueso-Barroso, Ana, Delgado, Julio, Moia, Riccardo, Ruiz-Gil, Sara, Marchese, Domenica, Giró, Ariadna, Verdaguer-Dot, Núria, Romo, Mónica, Clot, Guillem, Rozman, Maria, Frigola, Gerard, Rivas-Delgado, Alfredo, Baumann, Tycho, Alcoceba, Miguel, González, Marcos, Climent, Fina, Abrisqueta, Pau, Castellví, Josep, Bosch, Francesc, Aymerich, Marta, Enjuanes, Anna, Ruiz-Gaspà, Sílvia, López-Guillermo, Armando, Jares, Pedro, Beà, Sílvia, Capella-Gutierrez, Salvador, Gelpí, Josep Ll, López-Bigas, Núria, Torrents, David, Campbell, Peter J., Gut, Ivo, Rossi, Davide, Gaidano, Gianluca, Puente, Xose S., Garcia-Roves, Pablo M., Colomer, Dolors, Heyn, Holger, Maura, Francesco, Martín-Subero, José I., Campo, Elías

“…Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal…”
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The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities by Klus, Petr, Bolognesi, Benedetta, Agostini, Federico, Marchese, Domenica, Zanzoni, Andreas, Tartaglia, Gian Gaetano

“…The recent shift towards high-throughput screening is posing new challenges for the interpretation of experimental results. Here we propose the cleverSuite…”
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Repression of endogenous retroviruses prevents antiviral immune response and is required for mammary gland development by Avgustinova, Alexandra, Laudanna, Carmelo, Pascual-García, Mónica, Rovira, Quirze, Djurec, Magdolna, Castellanos, Andres, Urdiroz-Urricelqui, Uxue, Marchese, Domenica, Prats, Neus, Van Keymeulen, Alexandra, Heyn, Holger, Vaquerizas, Juan M., Benitah, Salvador Aznar

“…The role of heterochromatin in cell fate specification during development is unclear. We demonstrate that loss of the lysine 9 of histone H3 (H3K9)…”
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Systematic benchmarking of single-cell ATAC-sequencing protocols by De Rop, Florian V., Hulselmans, Gert, Flerin, Chris, Soler-Vila, Paula, Rafels, Albert, Christiaens, Valerie, González-Blas, Carmen Bravo, Marchese, Domenica, Caratù, Ginevra, Poovathingal, Suresh, Rozenblatt-Rosen, Orit, Slyper, Michael, Luo, Wendy, Muus, Christoph, Duarte, Fabiana, Shrestha, Rojesh, Bagdatli, S. Tansu, Corces, M. Ryan, Mamanova, Lira, Knights, Andrew, Meyer, Kerstin B., Mulqueen, Ryan, Taherinasab, Akram, Maschmeyer, Patrick, Pezoldt, Jörn, Lambert, Camille Lucie Germaine, Iglesias, Marta, Najle, Sebastián R., Dossani, Zain Y., Martelotto, Luciano G., Burkett, Zach, Lebofsky, Ronald, Martin-Subero, José Ignacio, Pillai, Satish, Sebé-Pedrós, Arnau, Deplancke, Bart, Teichmann, Sarah A., Ludwig, Leif S., Braun, Theodore P., Adey, Andrew C., Greenleaf, William J., Buenrostro, Jason D., Regev, Aviv, Aerts, Stein, Heyn, Holger

“…Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and…”
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